Publications of the CSL group2020
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PhD Thesis. Uncertainty quantification of multiscale models. ISBN 9789402819182. Supervised by A. G. Hoekstra and P. V. Coveney.
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Article. Sensitivity analysis based dimension reduction of multiscale models. Mathematics and Computers in Simulation 170, pp. 205-220.
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PhD Thesis. Microstructure dynamics in shear thickening suspensions. ISBN 9789402818611. Supervised by A. G. Hoekstra and D. Bonn.
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Article. Foreseeing the future of mutualistic communities beyond collapse. Ecology Letters 23(1), pp. 2-15.
2019
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PhD Thesis. The emergence of biofilms. Supervised by P. M. A. Sloot.
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Article. Shear thickening of dense suspensions: The role of friction. Physics of Fluids 31(10), 103103.
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Article. Semi-intrusive uncertainty propagation for multiscale models. Journal of Computational Science 35, pp. 80-90.
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Article. Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 2018154.
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Article. Science at the intersection of data, modelling, and computation. Journal of Computational Science 34, pp. 117-119.
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Article. Risk Factor Evolution for Counterparty Credit Risk under a Hidden Markov Model. Risks 7(2), 66.
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Article. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids 31(3), 031903.
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Article. Prediction and quantification of bacterial biofilm detachment using Glazier-Graner–Hogeweg method based model simulations. Journal of Theoretical Biology 482, 109994.
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Article. Patterns for High Performance Multiscale Computing. Future Generation Computer Systems 91, pp. 335-346.
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Proceedings. Optimizing Parallel Performance of the Cell Based Blood Flow Simulation Software HemoCell. In: Computational Science – ICCS 2019. ISBN 9783030227449. 3, pp. 537-547.
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Article. Multiscale modelling, simulation and computing: from the desktop to the exascale. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 20180355.
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Article. Multiscale computing for science and engineering in the era of exascale performance. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 20180144.
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Article. Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH)—phase II: rupture risk assessment. International Journal of Computer Assisted Radiology and Surgery 14(10), p. 1795–1804.
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Article. Modelling the Influence of Regional Identity on Human Migration. Urban Science 3(3), 78.
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Article. Modeling the effect of high calorie diet on the interplay between adipose tissue, inflammation and diabetes. Computational and Mathematical Methods in Medicine 2019, 7525834.
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Article. Medication management support in diabetes: a systematic assessment of diabetes self-management apps. BMC Medicine 17, 127.
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Article. Low and variable pH decreases recruitment efficiency in populations of a temperate coral naturally present at CO2 vent. Limnology and Oceanography 64(3), pp. 1059-1069.
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Article. Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments. Cardiovascular Engineering and Technology 10(4), p. 568–582.
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Proceedings. Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations. In: Computational Science – ICCS 2019. ISBN 9783030227470. IV, pp. 479-492.
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Article. Inferring causation from time series in Earth system sciences. Nature Communications 10, 2553.
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Article. Image Based Classification of Slums, Built-Up and Non-Built-Up Areas in Kalyan and Bangalore, India. European Journal of Remote Sensing 52(S1), pp. 40-61.
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Article. Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer. Journal of the Royal Society Interface 16(159), 20190148.
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Article. Game of neutrophils: modeling the balance between apoptosis and necrosis. BMC Bioinformatics 20(Suppl 6), p. 475.
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Article. Finding the direction of lowest resilience in multivariate complex systems. Journal of the Royal Society Interface 16(159), 20190629.
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Article. Deprivation pockets through the lens of convolutional neural networks. Remote Sensing of the Environment 234, 111448.
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Article. Complexiteit van ziekten Een moderne visie in tijden van vergrijzing en multimorbiditeit. Nederlands Tijdschrift voor Geneeskunde 163, D3970.
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Chapter. Calibrating the Mean-Reversion Parameter in the Hull-White Model Using Neural Networks. In: ECML PKDD 2018 Workshops. ISBN 9783030134631. pp. 23-36.
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Article. Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. BMC Systems Biology 13(Supplement 2), 36.
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Article. An exploratory factor analysis model for slum severity index in Mexico City. Urban Studies .
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Article. A Smartphone App to Improve Medication Adherence in Patients With Type 2 Diabetes in Asia. JMIR mHealth and uHealth 7(9), e14914.
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PhD Thesis. 3D modelling of in-stent restenosis. Supervised by A. G. Hoekstra, A. V. Boukhanovsky, and A. Svitenkov.
2018
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Proceedings. Vulnerability Of Charging Infrastructure, A Novel Approach For Improving Charging Station Deployment. In: Proceedings of 7th Transport Research Arena TRA 2018.
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Article. Virtual physiological human 2016: translating the virtual physiological human to the clinic. Interface Focus 8(1), 20170067.
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Article. Urgent computing for decision support in critical situations. Future Generation Computer Systems 79(1), pp. 111-113.
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Proceedings. Understanding Malaria Induced Red Blood Cell Deformation Using Data-Driven Lattice Boltzmann Simulations. In: Computational Science – ICCS 2018. ISBN 9783319936987. pp. 392-403.
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Article. Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis. Cardiovascular Engineering and Technology 9(4), pp. 761-774.
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PhD Thesis. Toward reverse engineering spatiotemporal gene regulatory networks of Nematostella vectensis. ISBN 9789402810110. Supervised by P. M. A. Sloot and J. A. Kaandorp.
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Article. The art of computational science: Bridging gaps – forming alloys. Journal of Computational Science 26, pp. 190-192.
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Article. The Virtual Physiological Human Conference 2016. Journal of Computational Science 24, pp. 65-67.
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Article. System dynamics of human body thermal regulation in outdoor environments. Building and Environment 143, pp. 760-769.
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Article. Survey-based socio-economic data from slums in Bangalore, India. Scientific Data 5, 170200.
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Article. Supplemented alkaline phosphatase supports the immune response in patients undergoing cardiac surgery: Clinical and computational evidence. Frontiers in Immunology 9, 2342.
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Article. Spatial segregation, inequality, and opportunity bias in the slums of Bengaluru. Cities : The International Journal of Urban Policy and Planning 74, pp. 269-276.
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Article. Quantification of complex modular architecture in plants. New Phytologist 218(2), pp. 859-872.
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PhD Thesis. Patterns for multiscale computing. ISBN 9789463234092. Supervised by P. M. A. Sloot and A. G. Hoekstra.
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Article. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences 8(9), 1616.
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Article. Multiscale Modeling: recent progress and open questions. Multiscale and Multidisciplinary Modeling, Experiments and Design 1(1), p. 57–68.
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Article. Morphogenesis in Robot Swarms. Science Robotics 3(25), eaau9178.
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Article. Modelling Neutrophils' Response to Various Levels of Insults. Procedia Computer Science 136, pp. 390-397.
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Article. Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism. Antimicrobial Agents and Chemotherapy 62(4), e02544-17.
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Article. Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science 24, pp. 1-7.
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Article. Liquidity risk in derivatives valuation: an improved credit proxy method. Quantitative Finance 18(3), pp. 467-481.
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Report. IvI Education vision.
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Article. Information processing features can detect behavioral regimes of dynamical systems. Complexity 2018, 6047846.
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Article. Inflow and outflow boundary conditions for 2D suspension simulations with the immersed boundary lattice Boltzmann method. Computers & fluids 172, p. 312–317.
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Article. Incorporating Contagion in Portfolio Credit Risk Models Using Network Theory. Complexity 2018, 6076173.
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Article. High-throughput method for extracting and visualizing the spatial gene expressions from in situ hybridization images: A case study of the early development of the sea anemone Nematostella vectensis. Gene expression patterns : GEP 27, pp. 36-45.
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Article. Financial statement networks: an application of network theory in audit. The Journal of Network Theory in Finance 4(4), pp. 59-85.
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Proceedings. Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. In: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine. ISBN 9781538654880, 9781538654873. pp. 1401-1405.
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Article. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sciences advances 4(6), eaar8028.
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Article. Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch. Proceedings of the National Academy of Sciences of the United States of America 115(14), pp. 3575-3580.
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Article. Coupling Game Theory and Discrete-Event Simulation for Model-Based Ambulance Dispatching. Procedia Computer Science 136, pp. 398-407.
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Article. Combined Lattice–Boltzmann and rigid-body method for simulations of shear-thickening dense suspensions of hard particles. Computers & fluids 172, pp. 474-482.
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Article. Cell-resolved blood flow simulations of saccular aneurysms: effects of pulsatility and aspect ratio. Journal of the Royal Society Interface 15(146), 20180485.
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Article. Categorical and Geographical Separation in Science. Scientific Reports 8, 8253.
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Article. Application of clustering methods for detecting critical acute coronary syndrome patients. Procedia Computer Science 136, pp. 370-379.
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Article. Analysis of publication activity of computational science society in 2001–2017 using topic modelling and graph theory. Journal of Computational Science 26, pp. 193-204.
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Article. A study on the dynamics of temporary HIV treatment to assess the controversial outcomes of clinical trials: An in-silico approach. PLoS ONE 13(7), e0200892.
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Article. A new hypothesis on the role of vessel topology in cerebral aneurysm initiation. Computers in Biology and Medicine 103, pp. 244-251.
2017
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Article. eHealth in the future of medications management: personalisation, monitoring and adherence. BMC Medicine 15, 73.
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Article. Uncertainty quantification and sensitivity analysis applied to the wind wave model SWAN. Environmental Modelling & Software 95, pp. 344-357.
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Article. The study of the influence of obstacles on crowd dynamics. Procedia Computer Science 108, pp. 215-224.
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Article. The effect of allometric scaling in coral thermal microenvironments. PLoS ONE 12(10), e0184214.
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Article. The Art of Computational Science, Bridging Gaps - Forming Alloys. Procedia Computer Science 108, pp. 1-6.
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Article. The Art of Computational Science, Bridging Gaps - Forming Alloys. Procedia Computer Science 108, pp. 1-2.
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Article. Scatter Search Applied to the Inference of a Development Gene Network. Computation 5(2), 22.
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Article. Revisiting the use of the immersed-boundary lattice-Boltzmann method for simulations of suspended particles. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 96(1), 013302.
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Article. Relaxing Synchronization in Parallel Agent-Based Road Traffic Simulation. ACM Transactions on Modeling and Computer Simulation 27(2), 14.
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Article. Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts. BMC Research Notes 10(1), 103.
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Article. Quantifying Synergistic Information Using Intermediate Stochastic Variables. Entropy 19(2), 85.
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PhD Thesis. Phase transitions in complex systems. Supervised by P. M. A. Sloot, A. G. Hoekstra, and R. Quax.
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Article. Novel approach to investigation of semiconductor MOCVD by microreactor technology. Journal of Physics. Conference Series 917, 032011.
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Article. Multiscale computing in the exascale era. Journal of Computational Science 22, pp. 15-25.
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Article. Multiscale Modelling and Simulation, 14th International Workshop. Procedia Computer Science 108, pp. 1811-1812.
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Chapter. More likely we would be ritually slaughtered. In: 43 Visions for Complexity. ISBN 9789813206854. pp. 65-66.
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Article. Models of Pedestrian Adaptive Behaviour in Hot Outdoor Public Spaces. Procedia Computer Science 108, pp. 185-194.
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Article. Modelling the impact of household life cycle on slums in Bangalore. Computers, Environment and Urban Systems 64, pp. 275-287.
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Article. Modelling the distance impedance of protest attendance. Physica A : Statistical Mechanics and its Applications 468, pp. 171-182.
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Book. International Conference on Computational Science, ICCS 2017.
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Article. Hemocell: a high-performance microscopic cellular library. Procedia Computer Science 108, pp. 159-165.
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Article. Efficient Estimation of Sensitivities for Counterparty Credit Risk with the Finite Difference Monte Carlo Method. Journal of Computational Finance 21(1), pp. 83-113.
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Article. Design and evaluation of a data-driven scenario generation framework for game-based training. IEEE Transactions on Computational Intelligence and AI in Games 9(3), pp. 213-226.
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Article. Data through the Computational Lens. Journal of Computational Science 20, pp. 81-84.
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Article. Cellular Level In-silico Modeling of Blood Rheology with An Improved Material Model for Red Blood Cells. Frontiers in Physiology 8, 563.
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Article. Automatic model construction for the behavior of human crowds. Applied Soft Computing 56, pp. 368-378.
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Article. Anomaly detection in earth dam and levee passive seismic data using support vector machines and automatic feature selection. Journal of Computational Science 20, pp. 143-153.